SAN CARLOS — The mysterious liquid potions that keep scientists at LS9 Inc. so busy at their crowded lab in San Carlos may be unrecognizable, but they might someday become the world’s two most valuable fuels: gasoline and diesel.

The Silicon Valley startup claims to have developed a new technique to make industrial-scale “designer biofuels” in the lab from the same ingredients as ethanol, such as corn or sugar cane.

The major difference is that the fuels will act as a direct replacement for gasoline or diesel, making them more valuable than a gasoline supplement like ethanol.

LS9’s biofuels are also designed to flow into the same pipes and gas tanks as gasoline, whereas ethanol must be trucked in.

When the company begins production on a commercial scale — which LS9 leaders say could happen within three to five years — every gallon of fuel they produce will replace a gallon of fuel produced by the burning of fossil fuels. They will also be the first company to take their science to the market.

“People already know where to go for gas. There’s a whole infrastructure that would be built around our products,” said Gregory Pal, senior director of corporate development for LS9, ticking off the benefits. “From our perspective, the goal is to bring the technology to market as quickly as possible in terms of something that’s already compatible.”

If the technology pans out, it would come at a welcome time for a market increasingly hungry for domestic sources of fuel. Pal says his products would start at around $50 a barrel in a market currently trading at record highs of more than $90 a barrel.

The company’s hopes center around a secret ingredient, a patented organism too small to be seen by the naked eye. When added to a fermentation tank containing sugar and other nutrients, the organism feeds on the materials and produces a viscous, yellow liquid similar to gasoline.

“As humans, we eat a bunch of food and it breaks down into carbohydrates,” said Pal, pointing to one the lab’s bubbling fermenters. “This is what they eat.”

A couple of cleaning stages later, the liquid comes out with the same energy content as diesel or crude. The crude could then be sold to a refinery like regular oil, where it would then be transformed into jet fuel, gasoline, plastics and other materials derived from petroleum.

The process has the added benefit of skipping the last step in ethanol production: No extra heat or energy is required to distill the ethanol from the water at the end of fermentation.

Like its magic potion, LS9 is in the midst of a transformation. The 25-person operation will shortly move to a much larger industrial space in South San Francisco and double its staff. The new facility will give the company the platform it needs to perfect its products as it seeks funding to construct a production plant big enough to pump out 100 million gallons a year — the size of an ethanol plant, according to Pal.

LS9 was founded in 2005 by two scientists and two venture capital firms, and has raised $20 million to date.

Former Stanford University plant biologist Chris Somerville had the notion of creating a new kind of “bio-petrol” as a step toward addressing the world’s energy crisis after helping write a report for the Department of Energy that explored the benefits and drawbacks of existing biofuels.

“I believe that LS9 eventually will be providing their technology to hundreds or thousands of facilities around the world — like a franchise. Instead of making ethanol, facilities will just switch over to making LS9-type fuel,” said Somerville, who has discontinued his relationship with the company since being selected to head the University of California, Berkeley’s new Energy Biosciences Institute, which is funded by British Petroleum.

There is one catch. Relying on crops of corn or sugarcane for the sugars and starches LS9 needs to make its products is to depend on a limited supply of source materials, and on the energy- and resource-intensive process of growing them. If LS9 were to use sugar cane alone, Pal acknowledged, there would only be enough sugar available right now to make enough biofuels to offset 30 percent of the world’s gasoline production.

The only way to make biofuels sustainable, scientists largely agree, is to switch over to using cellulosic plants instead — materials like switchgrass and fast-growing trees that are more naturally abundant and easier to process.

Somerville’s lab is one of two at UC Berkeley currently tasked with researching this technology. Pending a couple of breakthroughs, Somerville predicts that large-scale production of cellulosic biomass is no more than five years away.

Most crucially, LS9’s technology won’t help the company control the greenhouse gas-reducing emissions that come out of the tailpipes of the cars they fuel — not to mention non-greenhouse gas-inducing emissions, like carbon monoxide.

According to Professor Dan Sperling, director of the Institute of Transportation Studies at University of California, Davis, a company like LS9 can still provide a 40 percent to 80 percent net reduction in greenhouse gases just by virtue of avoiding the traditional oil and gas production model.

“Creating a molecule that looks more like gas and diesel is where the biofuels of the future will be,” said Sperling. “I think this is part of the solution… If they can pull it off, that’s great for all of us.”

Pal said LS9’s products are not meant to replace other promising renewable transportation technologies, such as developing electric cars and hydrogen fuel cells.

“There’s going to be a portfolio of energies…There isn’t going to be one silver bullet in solving these problems,” he said.